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Yorodumi- PDB-4tzs: Structure of C. elegans HTP-2 bound to HIM-3 closure motif, P2121... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4tzs | ||||||
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Title | Structure of C. elegans HTP-2 bound to HIM-3 closure motif, P212121 form | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / HORMA domain / Meiosis / Chromosome axis | ||||||
Function / homology | Function and homology information regulation of centriole-centriole cohesion / meiotic chromosome segregation / homologous chromosome segregation / synaptonemal complex assembly / homologous chromosome pairing at meiosis / synaptonemal complex / lateral element / reciprocal meiotic recombination / sister chromatid cohesion / condensed nuclear chromosome ...regulation of centriole-centriole cohesion / meiotic chromosome segregation / homologous chromosome segregation / synaptonemal complex assembly / homologous chromosome pairing at meiosis / synaptonemal complex / lateral element / reciprocal meiotic recombination / sister chromatid cohesion / condensed nuclear chromosome / chromosome / DNA binding Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Rosenberg, S.C. / Corbett, K.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Dev.Cell / Year: 2014 Title: The Chromosome Axis Controls Meiotic Events through a Hierarchical Assembly of HORMA Domain Proteins. Authors: Kim, Y. / Rosenberg, S.C. / Kugel, C.L. / Kostow, N. / Rog, O. / Davydov, V. / Su, T.Y. / Dernburg, A.F. / Corbett, K.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4tzs.cif.gz | 208.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4tzs.ent.gz | 170.8 KB | Display | PDB format |
PDBx/mmJSON format | 4tzs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tz/4tzs ftp://data.pdbj.org/pub/pdb/validation_reports/tz/4tzs | HTTPS FTP |
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-Related structure data
Related structure data | 4trkC 4tzjC 4tzlC 4tzmC 4tznC 4tzoC 4tzqC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28744.303 Da / Num. of mol.: 2 / Fragment: UNP residues 1-253 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: htp-2, CELE_Y73B6BL.2, Y73B6BL.2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLysS / References: UniProt: Q95XC8 #2: Protein/peptide | Mass: 2183.381 Da / Num. of mol.: 2 / Fragment: UNP residues 275-291 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: him-3, CELE_ZK381.1, ZK381.1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLysS / References: UniProt: G5EBG0 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.18 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 15-22% PEG 3350 / PH range: 7.5-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→40 Å / Num. obs: 21690 / % possible obs: 99 % / Redundancy: 6.6 % / Rsym value: 0.087 / Net I/σ(I): 15.8 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→39.039 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.35 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→39.039 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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